If you are taking a Galapagos Cruise or package, it is best if you book your domestic flights to/from Galapagos from Quito, Guayaquil or mixed route along with your cruise. This because cruises/tours must follow a pre-approved itinerary by the National Park’s Authorities, and all start their itinerary with specific arriving flights to the Islands, and cannot wait for stragglers arriving on different flights other than the one used by the rest of the group.
Catching a cruise when arriving on different flights that are delayed or arrive on different timings can be very expensive and in some cases, impossible, causing distress and unwanted non-refundable trip cancelations.
For this reason, all operators recommend booking your domestic flights along with your cruise/tour in accordance with the operation in order to avoid unfortunate events. Please click here for more details on logistic and getting to the Galapagos.